So, you hold Starfleet accountable for every rogue officer?
Was Sisko in this case a "rogue officer?"
Or was he acting within the authority granted him by Starfleet. When you place someone in a position of power, even if you aren't monitoring them second by second, you bear a on-going responsibility for their official decisions and actions.
Sisko was acting as a Starfleet officer all during "In the Pale Moonlight," not as a private citizen. Sisko was counseled by his subordinates on his plan, but none of them attempted to shut the plan down. This wasn't a spur of the moment thing, where the officers under Sisko's commander might have been caught up in the action. They had time to consider, and go over Sisko head to higher command.
Starfleet does bear responsibility for Sisko actions, and the extended results of his plan.